I think people are looking in the wrong direction for their comparisons. Instead of focusing on music (where ridiculous arguments like synth vs. orchestral keep popping up), why not focus on voices?
This is actually trickier than it sounds, since a lot of SNES games that had voice tracks didn't have those same tracks in their Genesis counterparts. For instance,
ClayFighter for SNES opened with a fully voiced intro song, while the Genesis version just had the music with no lyrics.
Or take Mortal Kombat III for both consoles (you can check the first two MKs as well, but they're missing a lot of voice tracks on Genesis. Part 3 is still missing voices on Genesis, but has more than the first two).
The grunts, screams, and voices are much clearer on SNES. The Genesis version just doesn't add up.
Same goes for Street Fighter II.
SNES killed Genesis in voices here too.
I'm not just picking and choosing here either. I honestly can't think of a single game where voice effects were stronger in the Genesis version than in the SNES version. I'm more than happy to be proven wrong though, so feel free to give examples.
In the end, both consoles had great games with great music. But if the question is which console had the superior sound hardware, the proof is in the voices. Music quality is in the ear of the beholder, but a shitty voice is a shitty voice.